[gmx-users] Umbrella Sampling Tutorial Question
agnivogromacs14 at gmail.com
Sat Nov 1 01:48:42 CET 2014
Firstly thanks to Dr. Lemkul for his immensely informative and helpful
tutorials. I am following the umbrella sampling tutorial for one of my
During the placement of the molecule inside the box , the tutorial tells us
to visualize in VMD. Now , upon visualizing I find that the 4 strands of
protofibril protein look separated.
Then we are to restrain one of the strands and pull the next stand in the
I can not understand how this is physically possible as the strands
"appear" to be "physically separated" and we proceed to calculate PMF based
on binding energy.
Kindly shed some light on this issue , please. Pardon for my ignorance.
Thanks & Regards
Grad Student, Iowa State University.
More information about the gromacs.org_gmx-users